Classic BMW in Plano hasn't given me any issues. But then again I just have small mods like intake and exhaust. I think as long as your mods don't cause any warranty problems, then there are no issues. For example, if they find an exhaust leak and you don't have an OEM exhaust there isn't much you can do! But the fact that you have an exhaust leak doesn't affect anything with a dead radio(I had a dead radio and they changed it no problems asked). Also, i've seen many modded cars there : ).
2009 128i Coupe Crimson Red
MODS: -Injen Intake-Magnaflow Exhaust-Carbon Fiber Spoiler - Carbon Fiber Grilles - OZ Ultraleggeras - CF Mirrors